A federal law passed earlier this month directing a massive $16.3-billion overhaul of the troubled Department of Veterans Affairs health care system also aims to put pressure on colleges to lower education costs for veterans.

A far-reaching federal audit of the Department of Veterans Affairs published Tuesday confirmed long treatment delays and deficiencies in its health care system, but found no proof that delays in care caused up to 40 veteran deaths at a Phoenix hospital.

With the veterans’ health care system embroiled in scandal and a new generation coming home from war, President Barack Obama sought Tuesday to reassure American veterans that the government is committed to taking care of them.

WASHINGTON — The VA problems discovered in the inspector general audit released Tuesday go far beyond the Phoenix hospital system. Staff across the country including top leadership and managers were found guilty of ethical lapses and responsible for delays in veteran care at hundreds of facilities. Here are some of the other significant audit findings:

Various hospitals and clinics used six distinct schemes to manipulate patient wait times, including keeping paper lists outside the official electronic schedule, listing next available slots as veterans’ desired appointment dates, and canceling and rescheduling solely to reduce the appearance of a wait.

Despite the widespread manipulation, top VA management waived a requirement requiring certification of scheduling practices at hospitals and clinics during 2012 and 2013, which could have uncovered the activity. A VA official present when the decision was made said medical facility directors put up “significant resistance” and were “concerned about certifying results that may be later found inaccurate” by the IG.

Instead of a certification, the VA allowed facility directors to do a self-review using a set checklist. Of 127 VA health care facilities that answered the self-review, 114 said they were in compliance and were identifying and avoiding inappropriate scheduling activities.

IG Investigations of wait-time manipulation at 93 facilities nationwide are still ongoing after hundreds of complaints were filed in recent months. The FBI and Department of Justice are also involved, meaning criminal charges are possible.

In the run-up to the ethics lapses around scheduling, the VA decided to eliminate its chief ethics officer overseeing the integrated network of health care facilities during a reorganization in 2011.

Loopholes in the VA’s Vista electronic scheduling system, which the IG called “old and cumbersome,” were exploited by staff to game wait times. A failed VA project to replace it spent 5 years and more than $75 million but “failed to deliver a useable product because of ineffective planning and oversight.” A new effort began in May 2013 has invested over $14 million in planning but “to date, no solicitations have been issued for a replacement scheduling system.”